Epistatic selection on a selfish supergene - drive, recombination, and genetic load.

Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive-the driver and the target-linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, () in the fruit fly, . In African populations, the predominant chromosome variant, , is characterized by two overlapping, paracentric inversions on chromosome arm and nearly perfect (~100%) transmission. We study the system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying , the main driving allele, and one or more factors within the double inversion. While most chromosomes are homozygous lethal, haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of haplotypes in different populations around the world and have implications for supergene evolution broadly.